The long-term goal of our study is to elucidate the molecular basis for host factors involved in maintaining microbial homeostasis and to develop novel approaches that prevent and treat inflammatory bowel diseases (IBD) by restoring host-microbe relationships. Reduced levels of vitamin D and its receptor VDR have been found in human IBD and experimental colitis. In colitis animal models, downregulation of VDR promotes the severity, extent, and duration of mucosal inflammation. We have shown that conditional removal of VDR in the intestinal epithelium made mice more susceptible to chemical injury and Salmonella-colitis. Our recent Gut paper has demonstrated that intestinal epithelial VDR conditional knockout (VDR?IEC) leads to dysbiosis. However, how intestinal epithelial VDR is involved in maintaining microbial homeostasis and innate immunity remains largely unknown. The objective of this application is to study special consequences of VDR deficiency in Paneth cells and dysbiosis in the inflamed states. We study Paneth cells because: 1) the Paneth cells sense microbes and secrete anti-microbial peptides (AMPs); 2) the roles of Paneth cells are dependent on a functional autophagy pathway, which is essential in innate immunity and microbial ecology; and 3) a lack of ATG16L1, an IBD risk genes, leads to abnormal Paneth cells in the intestine. Intriguingly, we are the first to report that ATG16L1 is a target gene of VDR. Th absence of intestinal epithelial VDR is accompanied by a reduction in the mRNA and protein levels of ATG16L1. Therefore, we hypothesize that intestinal epithelial VDR is a determinant of IBD risk through its actions on Paneth cell functions and microbial assemblage in intestinal homeostasis. We have now developed novel experimental models to investigate VDR actions that critically affect host functions and microbiota of the intestine. Aim 1 will test the working hypothesis that intestinal epithelial VDR determines the function of Paneth cells and autophagy, thus changing gut microbiota in inflammation. We will A) elucidate how intestinal epithelial VDR leads to abnormal Paneth cells (impaired differentiation and decreased AMPs), in VDR?IEC and VDR?paneth cell mice; B) determine effects and mechanisms of VDR on autophagy regulators through apoptosis/autophagy balance, using organoids and VDR transgenic mice; and C) investigate whether over-expression of intestinal VDR restores Paneth cells and autophagy, using organoids and Tg-I-VDR mice. Aim 2 will test the working hypothesis that regulating the microbiome and restoring balance in VDR functions and the microbiome will restore function of Paneth cells and autophagy, thus reducing severity of colitis. We will: A) investigate the role of intestinal epithelial VDR in altering bacterial populations when administered via fecal transplantation or recolonization in originally germ-free mice; and B) define the effect and mechanism of forced intestinal VDR expression in restoring microbial homeostasis though Paneth cell and autophagy regulation in IL10-/- colitis mice. Our studies are innovative because they provide a unifying hypothesis that can potentially account for defective autophagy, abnormal Paneth cells, and dysbiosis found in many patients with IBD and intestinal disorders. These insights will lead to novel strategies to prevent and treat IBD and intestinal disorders.